
CPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)
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| Date/time: 06/05/24 15:17:10
| Available memory: 120.209 MB

	Reading 'COM.prmtop' as Amber Topology
	CHAMBER topology:
                                 CHARMM force field: No FF information parsed...
	Radius Set: H(N)-modified Bondi radii (mbondi2)
INPUT: Reading input from 'STDIN'
  [trajin COM_traj_0.xtc 10 48010 1000]
	Reading 'COM_traj_0.xtc' as Gromacs XTC
Warning: Trajectory box type is 'Triclinic' but topology box type is 'None'.
Warning: Setting topology box information from trajectory.
  [noprogress]
	Progress bar will not be used during Run.
  [rmsd !(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) mass first]
    RMSD: (!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)), reference is first frame (!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)), mass-weighted.
	Best-fit RMSD will be calculated, coords will be rotated and translated.
  [outtraj _GMXMMPBSA_complex.pdb pdb onlyframes 1 nobox]
	Saving frames 1
	Writing '_GMXMMPBSA_complex.pdb' as PDB
    OUTTRAJ: Writing frames associated with topology 'COM.prmtop'
  [outtraj _GMXMMPBSA_dummycomplex.inpcrd restart onlyframes 1 nobox]
	Saving frames 1
	Writing '_GMXMMPBSA_dummycomplex.inpcrd' as Amber Restart
    OUTTRAJ: Writing frames associated with topology 'COM.prmtop'
  [outtraj _GMXMMPBSA_complex.mdcrd.0 onlyframes 1-50 nobox]
Warning: Format not specified and extension '.0' not recognized. Defaulting to Amber Trajectory.
	Saving frames 1-50
	Writing '_GMXMMPBSA_complex.mdcrd.0' as Amber Trajectory
    OUTTRAJ: Writing frames associated with topology 'COM.prmtop'
  [strip :119-238]
    STRIP: Stripping atoms in mask [:119-238]
  [outtraj _GMXMMPBSA_receptor.pdb pdb onlyframes 1 nobox]
	Saving frames 1
	Writing '_GMXMMPBSA_receptor.pdb' as PDB
    OUTTRAJ: Writing frames associated with topology 'COM.prmtop'
  [outtraj _GMXMMPBSA_dummyreceptor.inpcrd restart onlyframes 1 nobox]
	Saving frames 1
	Writing '_GMXMMPBSA_dummyreceptor.inpcrd' as Amber Restart
    OUTTRAJ: Writing frames associated with topology 'COM.prmtop'
  [outtraj _GMXMMPBSA_receptor.mdcrd.0 onlyframes 1-50 nobox]
Warning: Format not specified and extension '.0' not recognized. Defaulting to Amber Trajectory.
	Saving frames 1-50
	Writing '_GMXMMPBSA_receptor.mdcrd.0' as Amber Trajectory
    OUTTRAJ: Writing frames associated with topology 'COM.prmtop'
  [unstrip]
  [rmsd !(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) mass first]
    RMSD: (!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)), reference is first frame (!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)), mass-weighted.
	Best-fit RMSD will be calculated, coords will be rotated and translated.
  [strip :1-118]
    STRIP: Stripping atoms in mask [:1-118]
  [outtraj _GMXMMPBSA_ligand.pdb pdb onlyframes 1 nobox]
	Saving frames 1
	Writing '_GMXMMPBSA_ligand.pdb' as PDB
    OUTTRAJ: Writing frames associated with topology 'COM.prmtop'
  [outtraj _GMXMMPBSA_dummyligand.inpcrd restart onlyframes 1 nobox]
	Saving frames 1
	Writing '_GMXMMPBSA_dummyligand.inpcrd' as Amber Restart
    OUTTRAJ: Writing frames associated with topology 'COM.prmtop'
  [outtraj _GMXMMPBSA_ligand.mdcrd.0 onlyframes 1-50 nobox]
Warning: Format not specified and extension '.0' not recognized. Defaulting to Amber Trajectory.
	Saving frames 1-50
	Writing '_GMXMMPBSA_ligand.mdcrd.0' as Amber Trajectory
    OUTTRAJ: Writing frames associated with topology 'COM.prmtop'
  [unstrip]
  [rmsd !(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) mass first]
    RMSD: (!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)), reference is first frame (!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)), mass-weighted.
	Best-fit RMSD will be calculated, coords will be rotated and translated.
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES (1 total):
 0: COM.prmtop, 3550 atoms, 238 res, box: Triclinic, 2 mol

INPUT TRAJECTORIES (1 total):
 0: 'COM_traj_0.xtc' is a GROMACS XTC file, Parm COM.prmtop (Triclinic box) (reading 49 of 50001)
  Coordinate processing will occur on 49 frames.

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'COM.prmtop' (16 actions):
  0: [rmsd !(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) mass first]
	Target mask: [!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)](3550)
	Reference topology: COM.prmtop
	Reference mask: [!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)](3550)
  1: [outtraj _GMXMMPBSA_complex.pdb pdb onlyframes 1 nobox]
        '_GMXMMPBSA_complex.pdb' is a PDB file, Parm COM.prmtop no box info,: Writing frames 1
	Has coordinates, time
  2: [outtraj _GMXMMPBSA_dummycomplex.inpcrd restart onlyframes 1 nobox]
        '_GMXMMPBSA_dummycomplex.inpcrd' is an AMBER restart file, Parm COM.prmtop no box info,: Writing frames 1
	Has coordinates, time
  3: [outtraj _GMXMMPBSA_complex.mdcrd.0 onlyframes 1-50 nobox]
        '_GMXMMPBSA_complex.mdcrd.0' is an AMBER trajectory, Parm COM.prmtop no box info,: Writing frames 1-50
	Has coordinates, time
  4: [strip :119-238]
	Stripping 1789 atoms.
	Stripped topology: 1761 atoms, 118 res, box: Triclinic, 1 mol
  5: [outtraj _GMXMMPBSA_receptor.pdb pdb onlyframes 1 nobox]
        '_GMXMMPBSA_receptor.pdb' is a PDB file, Parm COM.prmtop no box info,: Writing frames 1
	Has coordinates, time
  6: [outtraj _GMXMMPBSA_dummyreceptor.inpcrd restart onlyframes 1 nobox]
        '_GMXMMPBSA_dummyreceptor.inpcrd' is an AMBER restart file, Parm COM.prmtop no box info,: Writing frames 1
	Has coordinates, time
  7: [outtraj _GMXMMPBSA_receptor.mdcrd.0 onlyframes 1-50 nobox]
        '_GMXMMPBSA_receptor.mdcrd.0' is an AMBER trajectory, Parm COM.prmtop no box info,: Writing frames 1-50
	Has coordinates, time
  8: [unstrip]
  9: [rmsd !(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) mass first]
	Target mask: [!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)](3550)
	Reference topology: COM.prmtop
	Reference mask: [!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)](3550)
  10: [strip :1-118]
	Stripping 1761 atoms.
	Stripped topology: 1789 atoms, 120 res, box: Triclinic, 1 mol
  11: [outtraj _GMXMMPBSA_ligand.pdb pdb onlyframes 1 nobox]
        '_GMXMMPBSA_ligand.pdb' is a PDB file, Parm COM.prmtop no box info,: Writing frames 1
	Has coordinates, time
  12: [outtraj _GMXMMPBSA_dummyligand.inpcrd restart onlyframes 1 nobox]
        '_GMXMMPBSA_dummyligand.inpcrd' is an AMBER restart file, Parm COM.prmtop no box info,: Writing frames 1
	Has coordinates, time
  13: [outtraj _GMXMMPBSA_ligand.mdcrd.0 onlyframes 1-50 nobox]
        '_GMXMMPBSA_ligand.mdcrd.0' is an AMBER trajectory, Parm COM.prmtop no box info,: Writing frames 1-50
	Has coordinates, time
  14: [unstrip]
  15: [rmsd !(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) mass first]
	Target mask: [!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)](3550)
	Reference topology: COM.prmtop
	Reference mask: [!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)](3550)
----- COM_traj_0.xtc (10-48010, 1000) -----

Read 49 frames and processed 49 frames.
TIME: Avg. throughput= 35.3917 frames / second.

ACTION OUTPUT:
    OUTTRAJ: '_GMXMMPBSA_complex.pdb': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_dummycomplex.inpcrd': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.0': Wrote 49 frames.
    OUTTRAJ: '_GMXMMPBSA_receptor.pdb': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_dummyreceptor.inpcrd': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_receptor.mdcrd.0': Wrote 49 frames.
    OUTTRAJ: '_GMXMMPBSA_ligand.pdb': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_dummyligand.inpcrd': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_ligand.mdcrd.0': Wrote 49 frames.
TIME: Analyses took 0.0000 seconds.

DATASETS (3 total):
	RMSD_00001 "RMSD_00001" (double, rms), size is 49 (0.392 kB)
	RMSD_00002 "RMSD_00002" (double, rms), size is 49 (0.392 kB)
	RMSD_00003 "RMSD_00003" (double, rms), size is 49 (0.392 kB)
    Total data set memory usage is at least 1.176 kB

RUN TIMING:
TIME:		Init               : 0.0001 s (  0.01%)
TIME:		Trajectory Process : 1.3845 s ( 99.93%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0000 s (  0.00%)
TIME:		Data File Write    : 0.0000 s (  0.00%)
TIME:		Other              : 0.0007 s (  0.00%)
TIME:	Run Total 1.3854 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 1.7062 seconds.
--------------------------------------------------------------------------------
To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
  Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
  Theory Comput., 2013, 9 (7), pp 3084-3095.

